VMD-L Mailing List

From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Mon Feb 05 2024 - 00:01:55 CST

Hi, I have followed the Shape-Based Coarse Graining tutorial, and every step works for me up to the Obtaining initial guess for bonded interaction parameters from all-atom simulations step. I ran a 10 ns all-atom simulation of my protein in a waterbox NaCl. When I try to extract bond and angle params to begin the iterative param refinement, the Kb column in the .par file gets filled with "inf" and the .dat outputs get filled with "inf" in the last column. I am using VMD 1.9.4a55 on Linux. Why are they getting filled with "inf" and not values from the input files? Thanks!